Hidradenitis suppurativa (HS) is a common, debilitating inflammatory skin disease linked to immune dysregulation and abnormalities in follicular structure and function. The study we looked at tries to derive an expression-based HS disease signature by observing affected and unaffected skin from 20 subjects and characterize a transcriptomic profile through RNASeq. Differential expression and pathway enrichment analyses were then performed, and the results were compared to previously reported datasets.
We obtained the RNASeq data used for the study - A Hidradenitis Suppurativa Molecular Disease Signature Derived from Patient Samples by High-Throughput RNA Sequencing, available on GEO RNASeq results for 40 samples - and tried to replicate the differential expression profiling and pathway enrichment analyses.
Trace the Flow of the Project
Load
We read the data from GSE151243
# Loading the datapath_gene ="../data/_raw/GSE151243_Raw_gene_counts_matrix.txt"path_meta ="../data/_raw/GSE151243_series_matrix.txt"gene_table <-read.table(path_gene, header =TRUE)meta_table <-read.table(path_meta, skip =33, fill =TRUE, header =TRUE)
Data Cleaning
Start with 58051 genes in the pool
Remove gene if 0 expression for all patients (-6098)
Remove gene if expression linear model coefficient not significant between diseased/healthy tissue (p>0.05) (-51437)
Remove gene if expression change for all patients < 3-fold between the diseased/healthy tissue groups ( -29)
487 genes advance to analysis rounds
Materials and Methods
Results
Principal Component Analysis
Score Plot
Variance Explained
Most Upregulated and Downregulated Genes
Functional Assessment of Upregulated and Downregulated Genes
Upregulated genes:
NTRK1: Neuronal survival and Signal Transduction\n(MAPK, PI3K-Akt, PLC-\(\gamma\))
POU2AF1: B-Cell immune responds
SIGLEC7: Inhibition of NK-Cell responds
Downregulated genes:
KRT77: Kreatin, Intermediate filament protein
CHRM1: Muscarinic receptor
PHYHIP: Fatty acid metabolism and perioxisomal function
Enhanced Activation of Inflammatory, Innate and Adaptive immune pathway
Reduced Activity in Hair, Skin and Neural Cell Division Pathways
Discussion
Observations by Freudenberg et al.
Gene Upregulation
MMP1, C-X-C, SERPINB4, and S100.
Enhanced Immune Responses
Upregulation in both adaptive and innate immune system functions.
Reduced Keratinization and Intermediate Filament Activity
Potential Causes for Variance in Results
Model Selection
lm vs glm, Empirical Bayes
Adjusted P-value Cutoff Choices
Gene Selection Criteria
Focus only on protein-encoding genes
Chromosome Distribution of Upregulated genes
Chromosome Distribution of Downregulated genes
Read Counts are higher for Raw genes
Some nonlesional samples have higher read counts of Significant genes